Illumina'S Genome Studio Final Report: Forward Or Top Allele?

Question

[Mau]

I would like to know which columns should I read to get the correct allele calls in the Final Report file generated by Genome Studio Genotyping module.

Among others, I have the following columns:
Allele1 - Forward Allele2 - Forward Allele1 - Top Allele2 - Top.

I can see that the allele calls in TOP/BOT definitions are in the columns Allele2 - AB Allele1 - AB

But what is the SNP and what are the real nucleotides called for a given SNP Name?

Answer 1

[Xianjun]

For those who are still not clear with the difference columns in the FinalReport.txt (from GenomeStudio), e.g. Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2 - Top, Allele1 - Plus, Allele2 - Plus, a short answer is: TOP/BOT is for Illumina's own strand designations (which is pretty smart, but not popular), Forward/Reverse is same as the one used in dbSNP, and Plus/Minus is same as the one used in 1000 Genome. For details, see this page: https://my.illumina.com/MyIllumina/Bulletin/AsrDAlFpsEOrKneoUnHc0w/dna-strand-designations (for member only. But please allow me to paste here for clarification purpose only).

DNA Strand Designations

Jun 9 2016

Customer Strand:Same as the Source strand. For custom content, it is the strand submitted by the customer for probe design.

ILMN Strand, a.k.a. Design Strand: The strand used by Illumina to design probes based on thermodynamic stability and locus specificity according to NCBI BLAST. For this reason, it can differ from the Customer/ Source strand.

Forward/Reverse (Fwd/Rev) Strand: Used by dbSNP, Fwd/Rev designations can change with NCBI Genome Build updates, so Genome Build must be specified when reporting Fwd/Rev strands. 1. For SNPs in standard array products, Fwd strand = Source strand, and originates from dbSNP. 2. For custom array product SNPs without rsid’s, the customer can identify the Source strand as Fwd or Rev, based on their own criteria. Illumina custom product files use the customer’s Fwd/Rev designations. Note: The Fwd strand, as identified in Illumina standard product files, should not be confused with Plus (+) strand, which HapMap interchangeably calls the “forward strand.”

Plus/Minus (+/-) Strand: The standard designation for all eukaryotic organisms used by HapMapand 1000 Genomes Project. The 5′ end of the (+) strand is at the tip of the short arm (p arm) of the chromosome and the 5′ end of the (-) strand is at the tip of the long arm (q arm). (+/-) designations can change with NCBI Genome Build updates, so Genome Build must be specified when reporting (+/-) strands.

Source Strand: Same as the Customer strand. The strand submitted to the Illumina designer for probe design. 1. For standard SNPs, it is the Fwd strand as reported in the source database (i.e., dbSNP). 2. Custom content can be reported as rsid’s or as the DNA sequences or chromosomal regions, depending on the format submitted by the customer.

Top/Bottom (Top/Bot) Strand:Top/Bot nomenclature was developed by Illumina using sequence-based context to assign strand designations that does not change regardless of database or genome assembly used. (e.g., depending on the NCBI Genome Build referenced, strand and allele designations can change). Top/Bot is not directly related to Fwd/Rev or (+/-).Top/Bot strand is determined by examining the SNP and the surrounding DNA sequence and it only applies to SNPs with two possible alleles. See the Top/Bot A/B Allele bulletin for more details.

I also have a blog post for this confusion. It's helpful to read if you have similar question: http://onetipperday.sterding.com/2015/12/snp-allele-coding-schema.html

Answer 2

[Jan Oosting]

Illumina have a document that explains their naming conventions for SNPs Top/Bottom